On November 4, 2019 Paragon Genomics, Inc., a leader in amplicon-based target enrichment solutions for next-generation sequencing (NGS), reported the upcoming introduction of two new products at the 2019 Association for Molecular Pathology (AMP) Annual Meeting & Expo—a CleanPlex CFTR Panel for cystic fibrosis and CleanPlex Fusion Detection Methods for the diagnostic and prognostic assessment of cancer tumor progression (Press release, Paragon Genomics, NOV 4, 2019, View Source [SID1234550256]).

Schedule your 30 min Free 1stOncology Demo!
Discover why more than 1,500 members use 1stOncology™ to excel in:

Early/Late Stage Pipeline Development - Target Scouting - Clinical Biomarkers - Indication Selection & Expansion - BD&L Contacts - Conference Reports - Combinatorial Drug Settings - Companion Diagnostics - Drug Repositioning - First-in-class Analysis - Competitive Analysis - Deals & Licensing

                  Schedule Your 30 min Free Demo!

The CFTR Panel leverages Paragon Genomics’ CleanPlex technology in a multiplex PCR-based targeted resequencing assay designed to simplify the evaluation of somatic and germline variants across the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Mutations in this gene cause the devastating disease cystic fibrosis, and more than 1700 mutations have been identified to date. Different mutations affect functioning of the CFTR gene in different ways, so a comprehensive assessment is essential for determining optimal treatment. The CleanPlex CFTR Panel covers all exons of the CFTR gene and includes the important American College of Medical Genetics (ACMG)-recommended mutations, in a rapid and easy-to-use format.

Paragon Genomics also announced early access to its CleanPlex Fusion Detection Methods for known and novel gene fusions. At present, scientists have identified more than 21,000 gene fusions in almost all main subtypes of human cancers. Fusion genes, which often are oncogenes, contribute to tumor formation. The identification of fusion genes can serve as diagnostic and prognostic markers of tumor progression. The CleanPlex Fusion Detection Methods are built upon Paragon Genomics’ key ultra-high multiplex PCR and PCR background cleaning technologies, enabling the detection of fusion genes with or without known breakpoints in a rapid and easy-to-use format. Early access to the first panel, a Lung Cancer Fusion Panel, is now open, and the company will start to provide additional panel products along with a custom fusion assay design service towards the end of this year.

Paragon Genomics is sponsoring a Corporate Workshop at AMP 2019, Precision Medicine Powered by a Rapid, Flexible, and Scalable Target Enrichment Technology, on November 6 from 12:00-12:50 pm in Room 318-320 at the Baltimore Convention Center. Presentations by internal and external scientists will include discussions of the ultra-high multiplexed, rapid CleanPlex TMB panel; a CleanPlex custom 180-gene pharmacogenomics NGS panel; and CleanPlex-powered targeted sequencing of single circulating tumor cells for liquid biopsy applications retrieved using the RareCyte platform. Click here to register.

Paragon Genomics researchers are presenting a poster1 at AMP 2019 demonstrating the utility of its CleanPlex TMB Panel, an ultra-high multiplexed amplicon based NGS target enrichment approach for accurate, rapid and comprehensive TMB profiling, covering all the exons of 500 genes in a robust assay. Additionally, Paragon Genomics’ collaborator, RareCyte, is presenting a poster2 showing how the CleanPlex technology facilitates targeted sequencing of single circulating cancer cells retrieved using the RareCyte platform for liquid biopsy applications.

Tao Chen, CEO of Paragon Genomics, commented, "It’s gratifying to participate in a major industry event like AMP 2019 with important new products for our growing customer base. Our CleanPlex technology has the potential to make NGS-based genomic analyses across a wide variety of applications faster, easier, more accurate, more economical and more feasible. We look forward to sharing our latest advances with customers and colleagues in the coming days."

Paragon Genomics’ CleanPlex is a proprietary, ultra-high multiplexed NGS target enrichment technology featuring an innovative PCR background cleaning chemistry that allows tens of thousands of amplicons to be multiplexed in a single reaction pool, allowing a large number of targets to be interrogated in a single assay. The CleanPlex technology is available as ready-to-use panels or as customized assays designed and optimized using the company’s advanced panel design algorithm. For more information, contact [email protected].

1 – AMP Poster Program #ST061: Assessment of Tumor Mutational Burden Using a Rapid, Amplicon-Based NGS Target Enrichment Strategy for Accurate and Comprehensive Tumor Profiling, Exhibit Hall, Nov. 9, 2019, Session: Solid Tumors, 9:45–10:45 am.

2 – AMP Poster Program #1009: Amplicon-based Targeted Sequencing of Single Circulating Tumor Cell, Exhibit Hall, Nov. 9, 2019, Session: Informatics, 9:45–10:45 am. Presented by RareCyte, Inc.

Paragon Genomics’ CleanPlex products are for Research Use Only.

On November 4, 2019 Aeglea BioTherapeutics, Inc. (NASDAQ:AGLE), a clinical-stage biotechnology company that engineers next-generation human enzymes to provide solutions for diseases with unmet medical need, reported two additions to its senior management team (Press release, Aeglea BioTherapeutics, NOV 4, 2019, View Source [SID1234550273]). The Company welcomes Dr. Ravi M. Rao as chief medical officer and Michael C. Hanley as chief commercial officer.

Schedule your 30 min Free 1stOncology Demo!
Discover why more than 1,500 members use 1stOncology™ to excel in:

Early/Late Stage Pipeline Development - Target Scouting - Clinical Biomarkers - Indication Selection & Expansion - BD&L Contacts - Conference Reports - Combinatorial Drug Settings - Companion Diagnostics - Drug Repositioning - First-in-class Analysis - Competitive Analysis - Deals & Licensing

                  Schedule Your 30 min Free Demo!

"These appointments add important drug-development and commercial expertise to our leadership team as we advance our lead investigational therapy of pegzilarginase for patients with Arginase 1 Deficiency through a pivotal Phase 3 trial, and move two rare-disease pipeline programs into clinical studies," said Anthony G. Quinn, M.B Ch.B, Ph.D., president and chief executive officer of Aeglea. "Ravi brings extensive experience from GlaxoSmithKline and Roche, and has led programs across specialties in all stages of development, registration and launch. Mike is an accomplished life sciences commercial executive with diverse rare disease experience, having a track record of balancing a strategic long-term view with short-term performance and execution."

Dr. Rao joins Aeglea from GlaxoSmithKline (GSK) where he served as Vice President, Global Medical Affairs Head, Immunology and Specialty Franchise, leading programs across a number of emerging disease areas, previously serving as the Head Unit Physician and a Medicine Development Leader in immune-inflammation R&D. Prior to GSK, he served as Group Medical Director, Product Development Immunology and Clinical Development Site Head at Roche, where he played an important role in leading activities for the global clinical development and subsequent approvals of a number of the company’s key late-phase programs. Ravi was an academic physician-scientist at Imperial College (London) and is a Member of the Royal College of Physicians, London. He received his MB. BChir from Cambridge University and his Ph.D. in vascular biology from Imperial College, completing a postdoctoral fellowship at Harvard Medical School.

Mr. Hanley was previously Vice President and U.S. Chief Commercial Officer for Esteve Pharmaceuticals. He also previously served as Group Vice President, Marketing, Americas and Asia Pacific, Orphan Business Unit for Horizon Therapeutics with P&L responsibility for the company’s rare disease portfolio. In all, Mr. Hanley has 20 years of commercial leadership experience in the life sciences industry. Mr. Hanley holds a B.B.A. in Marketing from the University of Notre Dame and an MBA in Management and Strategy, Marketing from Northwestern University Kellogg School of Management.

On November 2, 2019 Vaccibody AS, a clinical stage company focused on developing personalized neoepitope cancer vaccines to target solid tumors, reported that it will host its capital markets day on November 12 and is pleased to invite investors, analysts and press to presentations by the members of the company’s executive management team and by Ulrich Granzer, PhD, founder of Granzer Regulatory Consulting & Services (Press release, Vaccibody, NOV 2, 2019, View Source [SID1234550196]). Granzer has a wide range of experience in all aspects of drug development and regulatory affairs, with particular focus on bringing novel therapies to market.

Schedule your 30 min Free 1stOncology Demo!
Discover why more than 1,500 members use 1stOncology™ to excel in:

Early/Late Stage Pipeline Development - Target Scouting - Clinical Biomarkers - Indication Selection & Expansion - BD&L Contacts - Conference Reports - Combinatorial Drug Settings - Companion Diagnostics - Drug Repositioning - First-in-class Analysis - Competitive Analysis - Deals & Licensing

                  Schedule Your 30 min Free Demo!

Venue: Forskningsparken, Gaustadalléen 21, 0349 Oslo. Meeting room Faros.

Date: Tuesday, 12th November 2019

Agenda:

14.00-14.10 Introduction Michael Engsig
14.10-15.00 Update on the VB N-01 study including the clinical data Agnete Fredriksen
15.00-15.45 Status of the cancer vaccine field and development of novel immunotherapies Ulrich Granzer
15.45-16.05 Company update Michael Engsig
16.05-16.30 Questions & Answers All
16.30-17.30 Mingling, snacks and drinks All

On November 2, 2019 Veracyte, Inc. (Nasdaq: VCYT) reported new data that advance understanding of the frequency, positive predictive value and co-occurrence of genomic alterations that are targeted by newly available and investigational precision medicine therapies for thyroid cancer (Press release, Veracyte, NOV 2, 2019, View Source [SID1234550197]). The findings were enabled by Afirma Xpression Atlas analyses, which uses RNA sequencing, of Veracyte’s extensive biorepository of thyroid nodule fine needle aspiration (FNA) samples from patients undergoing evaluation for thyroid cancer. The data were presented this week during the 89th Annual Meeting of the American Thyroid Association (ATA).

Schedule your 30 min Free 1stOncology Demo!
Discover why more than 1,500 members use 1stOncology™ to excel in:

Early/Late Stage Pipeline Development - Target Scouting - Clinical Biomarkers - Indication Selection & Expansion - BD&L Contacts - Conference Reports - Combinatorial Drug Settings - Companion Diagnostics - Drug Repositioning - First-in-class Analysis - Competitive Analysis - Deals & Licensing

                  Schedule Your 30 min Free Demo!

In one study, researchers assessed the frequency of ALK, BRAF, NTRK and RET fusions in nearly 48,000 consecutive patients whose thyroid nodule FNA samples were deemed indeterminate, suspicious for malignancy or malignant (Bethesda III/IV, V and VI categories, respectively) by cytopathology. The researchers found that 425 (0.89 percent) of the FNA samples harbored one of the alterations, with NTRK fusions the most common at 0.38 percent, followed by RET (0.32 percent), BRAF (0.13 percent) and ALK (0.06 percent). Additionally, RNA whole transcriptome sequencing demonstrated differences in the prevalence of these four fusions across Bethesda categories, with Bethesda V being the highest.

"NTRK fusion inhibitors have received pan-cancer FDA approval and clinical trials have included selective inhibitors of ALK, BRAF, NTRK and RET, which makes their detection in patients with thyroid cancer of interest to physicians," said Mimi I. Hu, M.D., professor at The University of Texas MD Anderson Cancer Center, who presented the findings in a poster. "As our understanding of the role of genomics in thyroid cancer advances, this information offers the potential to optimize initial treatment, predict response to treatment and prioritize selective targeted therapy should systemic treatment be needed."

In another study, researchers evaluated the positive predictive value of the NTRK, RET, BRAF and ALK fusions in 58 patients with indeterminate thyroid nodules (Bethesda III/IV categories) from Veracyte’s biorepository for whom surgical pathology diagnoses were available. They found that NTRK and RET fusions were associated with malignancy in 28 of 30 nodules, while risk of malignancy was lower among nodules with ALK (67 percent) or BRAF (75 percent). In a third study, researchers found that when using RNA sequencing data on a large sample of nearly 48,000 thyroid nodule FNA samples (Bethesda categories III-VI), they identified 263 co-occurrences of gene fusions and variants that were previously considered "mutually exclusive."

"The findings from these three studies underscore the power of our extensive biorepository of thyroid nodule FNA samples and our optimized RNA sequencing platform to advance understanding of the genomic underpinnings of thyroid cancer and to better capture the biology of thyroid lesions," said Richard T. Kloos, M.D., senior medical director, endocrinology, at Veracyte. "As precision medicine therapies that target specific gene alterations emerge, understanding individual patients’ genomic profiles becomes increasingly important to physicians. Our Afirma Xpression Atlas provides this information at the same time as initial diagnosis with the Afirma Genomic Sequencing Classifier, or GSC, to help inform treatment decisions."

Also during the ATA meeting, Veracyte unveiled its new Afirma patient report, which in addition to identifying patients with benign or suspicious-for-cancer nodules among those deemed indeterminate by cytopathology, based on Afirma GSC results, now provides individualized and actionable variant and fusion information on each patient. This information includes: risk of malignancy, associated neoplasm type, relative risk of lymph node metastasis and extrathyroidal extension; availability of FDA-approved therapy; and genetic counseling and germline testing considerations. This information is also provided for patients with cytopathology results that are suspicious for malignancy or malignant (Bethesda V and VI).

About Afirma

The Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas provide physicians with a comprehensive solution for a complex landscape in thyroid nodule diagnosis. The Afirma GSC was developed with RNA whole-transcriptome sequencing and machine learning and helps identify patients with benign thyroid nodules among those with indeterminate cytopathology results in order to help patients avoid unnecessary diagnostic thyroid surgery. The Afirma Xpression Atlas provides physicians with genomic alteration content from the same fine needle aspiration samples that are used in Afirma GSC testing and may help physicians decide with greater confidence on the surgical or therapeutic pathway for their patients. The Afirma Xpression Atlas includes 761 DNA variants and 130 RNA fusion partners in over 500 genes that are associated with thyroid cancer.

On November 1, 2019 Minomic International Ltd reported that it has entered into a research collaboration agreement with Sienna Cancer Diagnostics Ltd (ASX: SDX) ("Sienna" or "the Company"), a medical technology company developing and commercialising innovative cancer-related tests, to develop a proprietary test for the early detection of pancreatic cancer (Press release, Minomic, NOV 1, 2019, View Source [SID1234550126]).

Schedule your 30 min Free 1stOncology Demo!
Discover why more than 1,500 members use 1stOncology™ to excel in:

Early/Late Stage Pipeline Development - Target Scouting - Clinical Biomarkers - Indication Selection & Expansion - BD&L Contacts - Conference Reports - Combinatorial Drug Settings - Companion Diagnostics - Drug Repositioning - First-in-class Analysis - Competitive Analysis - Deals & Licensing

                  Schedule Your 30 min Free Demo!

This will be the first application of Sienna’s capture technology that was acquired in April 2019. The general capture technology is trademarked as SIEN-NET and the specific exosome capture technology as EXO-NET. Sienna will provide EXO-NET beads which rapidly and specifically capture exosomes (nanoparticles shed from cells into the bloodstream) from blood and other body fluids.

Several independent studies have indicated that exosomes from pancreatic cancer patients contain a protein called glypican-1 (GPC-1). Minomic holds a strong intellectual property position around GPC-1 with four families of patents already completing Patent Cooperation Treaty applications. Based on the data, the companies have agreed to enter into a collaboration to conduct research to determine the feasibility of producing an assay for the accurate screening, diagnosis and prognosis of pancreatic cancer.

About pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is the most lethal cancer in humans, with a five-year survival rate of less than 10%. Cancer Australia estimates that 3,599 new cases of pancreatic cancer will be diagnosed in Australia in 2019[1]. Notably, due to the asymptomatic nature of early-stage pancreatic cancer and the lack of a non-invasive early-stage diagnostic assay, approximately 80–85% of cases at initial diagnosis present with unresectable advanced or metastatic disease. The median survival time for these patients is only 3–14 months[2].

A biomarker assay that can specifically detect asymptomatic premalignant or early malignant tumours and predict the response to treatment would greatly benefit these patients[3]. Minomic and Sienna aim to deliver such an assay through this collaboration.

"Minomic International Ltd is excited to work with Sienna to develop this opportunity to extend the use of our GPC-1 antibody beyond prostate cancer detection", said Minomic’s Chief Executive Officer Dr Brad Walsh.

"We are pleased to have entered into this collaboration with Minomic, and we are very hopeful that it will result in the development of a novel and reliable assay for the detection of pancreatic cancer to add to the company’s pipeline of cancer diagnostic tests. It is a perfect first application for our proprietary biomarker capture technology, SIEN-NET", said Sienna’s Chief Executive Officer, Carl Stubbings.

The companies will share the costs of the proof of concept stage of the development.

_____________________________

[1] View Source

[2] Lu H, Niu F, Liu F, Gao J, Sun Y, Zhao X. Elevated glypican-1 expression is associated with an unfavorable prognosis in pancreatic ductal adenocarcinoma. Cancer Med 2017; 6(6):1181–1191

doi: 10.1002/cam4.1064

[3] Qi Z-H, Xu H-X, Zhang S-R, Xu J-Z, Li S, Gao H-L, Jin W, Wang W-Q, Wu C-T, Ni Q-X, Yu X-J, Liu L.

The significance of liquid biopsy in pancreatic cancer. J Cancer 2018; 9(18): 3417-3426. doi: 10.7150/jca.24591